메뉴 건너뛰기




Volumn 197, Issue 1, 2014, Pages 389-399

A novel statistical approach for jointly analyzing RNA-Seq data from F1 reciprocal crosses and inbred lines

Author keywords

[No Author keywords available]

Indexed keywords

ALLELIC IMBALANCE; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CROSS BREEDING; DIPLOIDY; DNA BASE COMPOSITION; EXON; FEMALE; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENOME IMPRINTING; INBRED STRAIN; MALE; MOUSE; MOUSE STRAIN; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STOCHASTIC MODEL; X CHROMOSOME; X CHROMOSOME INACTIVATION; ANIMAL; BIOSTATISTICS; CHROMOSOME; GENETICS; HYBRIDIZATION; INBREEDING; PROCEDURES;

EID: 84901370025     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.113.160119     Document Type: Article
Times cited : (18)

References (24)
  • 1
    • 0035228079 scopus 로고    scopus 로고
    • X-chromosome inactivation: Counting, choice and initiation
    • Avner, P., and E. Heard, 2001 X-chromosome inactivation: counting, choice and initiation. Nat. Rev. Genet. 2: 59-67.
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 59-67
    • Avner, P.1    Heard, E.2
  • 2
    • 56349112904 scopus 로고    scopus 로고
    • Global survey of genomic imprinting by transcriptome sequencing
    • Babak, T., B. Deveale, C. Armour, C. Raymond, M. A. Cleary et al., 2008 Global survey of genomic imprinting by transcriptome sequencing. Curr. Biol. 18: 1735-1741.
    • (2008) Curr. Biol. , vol.18 , pp. 1735-1741
    • Babak, T.1    Deveale, B.2    Armour, C.3    Raymond, C.4    Cleary, M.A.5
  • 4
    • 0032714352 scopus 로고    scopus 로고
    • Genomic control for association studies
    • Devlin, B., and K. Roeder, 1999 Genomic control for association studies. Biometrics 55: 997-1004.
    • (1999) Biometrics , vol.55 , pp. 997-1004
    • Devlin, B.1    Roeder, K.2
  • 5
    • 19844366096 scopus 로고    scopus 로고
    • Cis-acting expression quantitative trait loci in mice
    • Doss, S., E. Schadt, T. Drake, and A. Lusis, 2005 Cis-acting expression quantitative trait loci in mice. Genome Res. 15: 681-691.
    • (2005) Genome Res. , vol.15 , pp. 681-691
    • Doss, S.1    Schadt, E.2    Drake, T.3    Lusis, A.4
  • 6
    • 84860231981 scopus 로고    scopus 로고
    • RNA studies under fire
    • Hayden, E. C., 2012 RNA studies under fire. Nature 484: 428.
    • (2012) Nature , vol.484 , pp. 428
    • Hayden, E.C.1
  • 7
    • 77955299096 scopus 로고    scopus 로고
    • High-resolution analysis of parent-of-origin allelic expression in the mouse brain
    • Gregg, C., J. Zhang, B. Weissbourd, S. Luo, G. P. Schroth et al., 2010a High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329: 643-648.
    • (2010) Science , vol.329 , pp. 643-648
    • Gregg, C.1    Zhang, J.2    Weissbourd, B.3    Luo, S.4    Schroth, G.P.5
  • 8
    • 77955285002 scopus 로고    scopus 로고
    • Sex-specific parent-of-origin allelic expression in the mouse brain
    • Gregg, C., J. Zhang, J. E. Butler, D. Haig, and C. Dulac, 2010b Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329: 682-685.
    • (2010) Science , vol.329 , pp. 682-685
    • Gregg, C.1    Zhang, J.2    Butler, J.E.3    Haig, D.4    Dulac, C.5
  • 9
    • 84869036699 scopus 로고    scopus 로고
    • Modelling and simulating generic RNA-Seq experiments with the flux simulator
    • Griebel, T., B. Zacher, P. Ribeca, E. Raineri, V. Lacroix et al., 2012 Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res. 40: 10073-10083.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 10073-10083
    • Griebel, T.1    Zacher, B.2    Ribeca, P.3    Raineri, E.4    Lacroix, V.5
  • 10
    • 77955343193 scopus 로고    scopus 로고
    • Cloud-scale RNA-sequencing differential expression analysis with Myrna
    • Langmead, B., K. D. Hansen, and J. T. Leek, 2010 Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 11: R83.
    • (2010) Genome Biol. , vol.11
    • Langmead, B.1    Hansen, K.D.2    Leek, J.T.3
  • 11
    • 84858041341 scopus 로고    scopus 로고
    • Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
    • McCarthy, D. J., Y. Chen, and G. K. Smyth, 2012 Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40: 4288-4297.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 4288-4297
    • McCarthy, D.J.1    Chen, Y.2    Smyth, G.K.3
  • 13
    • 84856103215 scopus 로고    scopus 로고
    • Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression
    • Okae, H., H. Hiura, Y. Nishida, R. Funayama, S. Tanaka et al., 2012 Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression. Hum. Mol. Genet. 21: 548-558.
    • (2012) Hum. Mol. Genet. , vol.21 , pp. 548-558
    • Okae, H.1    Hiura, H.2    Nishida, Y.3    Funayama, R.4    Tanaka, S.5
  • 14
    • 78650539308 scopus 로고    scopus 로고
    • From RNAseq reads to differential expression results
    • Oshlack, A., M. D. Robinson, and M. D. Young, 2010 From RNAseq reads to differential expression results. Genome Biol. 11: 220.
    • (2010) Genome Biol. , vol.11 , pp. 220
    • Oshlack, A.1    Robinson, M.D.2    Young, M.D.3
  • 15
    • 77950460661 scopus 로고    scopus 로고
    • Understanding mechanisms underlying human gene expression variation with RNA sequencing
    • Pickrell, J., J. Marioni, A. Pai, J. Degner, B. Engelhardt et al., 2010 Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
    • (2010) Nature , vol.464 , pp. 768-772
    • Pickrell, J.1    Marioni, J.2    Pai, A.3    Degner, J.4    Engelhardt, B.5
  • 17
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson, M. D., and A. Oshlack, 2010 A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11: R25.
    • (2010) Genome Biol. , vol.11
    • Robinson, M.D.1    Oshlack, A.2
  • 18
    • 48949094754 scopus 로고    scopus 로고
    • Local regulatory variation in Saccharomyces cerevisiae
    • Ronald, J., R. Brem, J. Whittle, and L. Kruglyak, 2005 Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet. 1: e25.
    • (2005) PLoS Genet. , vol.1
    • Ronald, J.1    Brem, R.2    Whittle, J.3    Kruglyak, L.4
  • 19
    • 80053522581 scopus 로고    scopus 로고
    • A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    • Skelly, D. A., M. Johansson, J. Madeoy, J. Wakefield, and J. M. Akey, 2011 A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res. 21: 1728-1737.
    • (2011) Genome Res. , vol.21 , pp. 1728-1737
    • Skelly, D.A.1    Johansson, M.2    Madeoy, J.3    Wakefield, J.4    Akey, J.M.5
  • 20
    • 84856753476 scopus 로고    scopus 로고
    • A statistical framework for eQTL mapping using RNA-seq data
    • Sun, W., 2012 A statistical framework for eQTL mapping using RNA-seq data. Biometrics 68: 1-11.
    • (2012) Biometrics , vol.68 , pp. 1-11
    • Sun, W.1
  • 21
    • 57149085481 scopus 로고    scopus 로고
    • Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    • 't Hoen, P. A. C., Y. Ariyurek, H. H. Thygesen, E. Vreugdenhil, R. H. A. M. Vossen et al., 2008 Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res. 36: e141.
    • (2008) Nucleic Acids Res. , vol.36
    • 't Hoen, P.A.C.1    Ariyurek, Y.2    Thygesen, H.H.3    Vreugdenhil, E.4    Vossen, R.H.A.M.5
  • 22
    • 57349168544 scopus 로고    scopus 로고
    • Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain
    • Wang, X., Q. Sun, S. D. McGrath, E. R. Mardis, P. D. Soloway et al., 2008 Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 3: e3839.
    • (2008) PLoS ONE , vol.3
    • Wang, X.1    Sun, Q.2    McGrath, S.D.3    Mardis, E.R.4    Soloway, P.D.5
  • 23
    • 57749195712 scopus 로고    scopus 로고
    • Rna-seq: A revolutionary tool for transcriptomics
    • Wang, Z., M. Gerstein, and M. Snyder, 2009 Rna-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10: 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 24
    • 80053451880 scopus 로고    scopus 로고
    • A powerful and flexible approach to the analysis of RNA sequence count data
    • Zhou, Y. H., K. Xia, and F. A. Wright, 2011 A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics 27: 2672-2678.
    • (2011) Bioinformatics , vol.27 , pp. 2672-2678
    • Zhou, Y.H.1    Xia, K.2    Wright, F.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.